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Observation of water molecules within the bimolecular ▫$d(G_3CT_4G_3C)_2 G-quadruplex$▫
Zavasnik, Jaka ; Podbevšek, Peter ; Plavec, Janez
G-Rich oligonucleotides with cytosine residues in their sequences can form G-quadruplexes where G-quartets are flanked by G C Watson-Crick base pairs. Inan attempt to probe the role of cations in ...stabilization of a structural element with two G C base pairs stacked on a G-quartet, we utilized solution state nuclear magnetic resonance to study the folding of the d(G3CT4G3C) oligonucleotide into a G-quadruplex upon addition of 15NH4+ ions. Its bimolecular structure exhibits antiparallel strands with edge-type loops. Two G-quartets in the core of the structure are flanked by a couple of Watson-Crick G C base pairs in a sheared arrangement. The topology is equivalent to the solution state structure of the same oligonucleotide in the presence of Na+ and K+ ions [Kettani, A., et al. (1998) J. Mol. Biol.282, 619,and Bouaziz, S., et al. (1998) J. Mol. Biol.282, 637). A single ammonium ion binding site was identified between adjacent G-quartets, but three sites were expected. The remaining potential cation binding sites between G-quartetsand G C base pairs are occupied by water molecules. This is the first observation of long-lived water molecules within a G-quadruplex structure. The flanking G C base pairs adopt a coplanar arrangement and apparently do not require cations to neutralize unfavorable electrostatic interactions among proximal carbonyl groups. A relatively fast movement of ammonium ions from the inner binding site to bulk with the rate constants of 21 s-1 was attributed to the lack of hydrogen bonds between adjacent G C base pairs and the flexibility of the T4 loops.
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